CHANGELOG.md

Change Log

0.7.3 (2017-12-29)

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Merged pull requests:

• Allow additional MAF columns #257 (tavinathanson)

0.7.2 (2017-12-28)

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Fixed bugs:

• ExonicSpliceSite with Subsitution/etc. alternate_effect is not included in filtering #255

0.7.1 (2017-09-01)

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Fixed bugs:

• all_effects caches, but does not return, all effects #253
• Don't cache after only top-priority effects; post-filter instead #252

Merged pull requests:

• Fix effects filtering for splice sites #256 (tavinathanson)

0.7.0 (2017-08-29)

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Fixed bugs:

• filter_fn result caching should work for Python 2 and 3 #174

Closed issues:

• ImportError: cannot import name 'AlleleParseError' #233
• Invalid RGBA argument error using plot\_survival #221
• support plotting survival curves for more than 2 groups #217
• Add cache\_root\_dir attribute #214
• Cache sometimes fails if user interrupts writing process #170
• builds against latest versions of isovar fails #69

Merged pull requests:

• Fix effect priority caching #254 (tavinathanson)
• add get-blob method to gcio #244 (jburos)
• add join\_on\_left parameter to dataframe_loader #242 (jburos)
• Expose gcloud utils #241 (jburos)
• Plot surv by strata #237 (jburos)
• allow median-vaf-purity with patients having no variants #236 (jburos)
• Fix mhcnames to v 0.1.0 #235 (jburos)
• "guess" at variant file format, if not obvious from filename #232 (jburos)
• Update warning and associated comment #230 (tavinathanson)
• Gcloud batch downloads #229 (jburos)
• Feature plot_survival by category (clean branch) #225 (jburos)
• Fix RGBA error with plot_survival #223 (jburos)
• Warn on vcf errors #222 (jburos)
• Google Storage file access add-on for cohorts (a.k.a. minibucket) #219 (armish)

0.6.4 (2017-06-05)

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Closed issues:

• median_vaf_purity() got an unexpected keyword argument 'normalized_per_mb' #212

Merged pull requests:

• add cache_root_dir attribute & behavior #216 (jburos)

0.6.3 (2017-05-28)

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Closed issues:

• Drop Python 2 support #204

Merged pull requests:

• small fix to address #212 #213 (jburos)

0.6.2 (2017-05-19)

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0.6.1 (2017-05-19)

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Merged pull requests:

• Add new PyPi server #210 (tavinathanson)

0.6.0 (2017-05-18)

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Closed issues:

• Not identifying filtered-cache-name in python 3 #195

Merged pull requests:

• Require Python 3 #208 (tavinathanson)
• Add optional show_progress #206 (tavinathanson)

0.5.5 (2017-05-16)

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Closed issues:

• TypeError: "load_maf() got an unexpected keyword argument 'encoding'" #203
• Solve intermittent test failures #201

Merged pull requests:

• Update Pageant logic #205 (tavinathanson)

0.5.4 (2017-04-29)

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Merged pull requests:

• Update encoding and str handling for Py2/3 compatibility #199 (tavinathanson)

0.5.3 (2017-04-05)

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Implemented enhancements:

• Add watermark for default filter_fn on Cohort initialization #183

Fixed bugs:

• deletion_count is counting all indels #182
• exonic_silent_snv_count is confusing #181

Closed issues:

• Don't allow PFS/OS values to be NaN? #193
• Add frameshift count function #191
• additional_data should automatically create Patient attributes #190
• Minor: old comment #184
• Number of functions is ballooning #173
• Support "merged" strelka VCF type #167
• Using only Strelka tier 1 results in divide by zero sometimes #166

Merged pull requests:

• Add patient __str__ #197 (tavinathanson)
• Fixing filter cache issues #196 (tavinathanson)
• Add a median VAF filter function and a filter_fn watermark #189 (tavinathanson)
• Refactor and fix functions #186 (tavinathanson)

0.5.2 (2017-01-18)

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Merged pull requests:

• Grab VAFs from MAFs #179 (tavinathanson)

0.5.1 (2017-01-17)

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Merged pull requests:

• Upgrade isovar to the latest version in cohorts #177 (tavinathanson)
• Pre-merge exonic counts into develop #172 (jburos)

0.5.0 (2016-12-17)

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Implemented enhancements:

• Create public-facing usage template #114

Merged pull requests:

• Add more granular variant specification and other minor changes #165 (tavinathanson)

0.4.2 (2016-11-30)

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Merged pull requests:

• Random MHC prediction for random cohort #164 (tavinathanson)
• Add variant generation to random_cohorts and more #161 (tavinathanson)

0.4.1 (2016-11-05)

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Fixed bugs:

• Single variant collections do not allow for metadata extraction #81
• Default to not requiring a single-value on dict #153 (tavinathanson)

Merged pull requests:

• Add regplot as a plot_correlation option #159 (tavinathanson)
• Simplify functions with decorators #158 (tavinathanson)

0.4.0 (2016-09-28)

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Implemented enhancements:

• Make API more consistent #150 (tavinathanson)

Closed issues:

• Update README w/ Tavi's bullet list of features and Jacki's TCGA demo #147
• Show plots in README's usage examples #141

Merged pull requests:

• Update pypi badge every 4 hours #151 (arahuja)
• Use conda to install pypandoc #149 (arahuja)
• Update README.md #148 (jburos)

0.3.0 (2016-09-27)

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Implemented enhancements:

• Break up load.py #37

Closed issues:

• pip install fails on v 0.2.0 #144
• Plot survival curves with upper/lower bounds #65

Merged pull requests:

• Ensure requirements and README.md is packaged #146 (arahuja)
• upgrade to varcode 0.5.1 and necessary deps #143 (arahuja)
• Add pypi badge #142 (arahuja)
• Fix versioneer settings #140 (tavinathanson)

0.2.0 (2016-09-21)

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Implemented enhancements:

• Split up load.py #138 (tavinathanson)
• Add barplot option to plot_joint and change plot_joint name to plot_correlation #134 (tavinathanson)
• Support joining on DataFrameLoaders with shared columns #132 (tavinathanson)
• Make benefit name configurable #131 (tavinathanson)
• Add float_str to round floats #128 (tavinathanson)
• Add default survival colors #126 (tavinathanson)
• Pass stat_func through jointplot #125 (tavinathanson)

Closed issues:

• Summarize provenance on init #80

Merged pull requests:

• Fix travis run #139 (tavinathanson)
• Add quickstart #136 (jburos)
• Allow boolean_value_map to be passed in to plot_benefit #133 (tavinathanson)
• Fix threshold formatting #130 (e5c)
• Fix fishers plot ranges #129 (arahuja)
• Allow configurable labels to survival plots #127 (arahuja)
• Fix survival plots for non-threshold conditions #123 (arahuja)

0.1.2 (2016-08-16)

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Implemented enhancements:

• Add p-value indicator #112 (tavinathanson)
• Make provenance printing optional #86 (tavinathanson)
• Filter to expressed variants #67 (tavinathanson)

Fixed bugs:

• Start plots at 0 on the y-axis #110
• Summarize_provenance fails after a cache has been deleted #92
• VariantCollection metadata is lost after filtering #66
• Caching issues #26
• Always use a boolean mask #118 (tavinathanson)
• Fix Fisher's exact plot for non-boolean columns #117 (tavinathanson)
• Fix travis failure #106 (tavinathanson)
• Fix expressed_missense_snv_count for None filter_fn #95 (tavinathanson)

Closed issues:

• too easy to over-ride cohort-level defaults #120
• Statistical significance * on mann whitney and fisher's exact plot #109
• Convert benefit labels #108
• filter_fn default works across variants and effects #100
• strip_column_names warning when running tests #89
• Default filter_fn back to None #77
• Spacing of new functions is off #73
• unit tests for summarize_provenance #71
• travis builds failing with isovar==0.0.6 #70
• Fix NaN situation #54
• Travis python2.7 build failing #53
• Handle null counts better #16

Merged pull requests:

• Add more to logrank results object #121 (tavinathanson)
• Allow labeling of response/benefit labels #111 (arahuja)
• Return namedtuples in plot functions #104 (tavinathanson)
• Remove flier from boxplot on stripboxplot #103 (arahuja)
• Add ax argument for fishers exact plot #102 (arahuja)
• Fix varcode at 0.4.15 until API updates #99 (arahuja)
• add load_kallisto() #98 (e5c)
• Fix warning messages on strip_column_names #94 (jburos)
• Fix minor bug in summarize_provenance #93 (jburos)
• Add filter_fn to Cohort #90 (tavinathanson)
• first draft of clean_column_names utility function #85 (jburos)
• Report data sources #84 (jburos)
• modify setup.py to reference requirements.txt #83 (jburos)
• Add basic bootstrap AUC and coxph to cohorts #79 (tavinathanson)
• Use filter_fn None as default #78 (tavinathanson)
• Add responder_pfs_equals_os options #75 (tavinathanson)
• Summarize provenance #68 (jburos)
• Fix threshold rounding #63 (arahuja)
• Display a rounded threshold #62 (arahuja)
• Updates to filtering #61 (tavinathanson)
• Add Pageant CoverageDepth output parsing #60 (tavinathanson)
• Add axes argument to roc plots #59 (arahuja)
• Pass along axes argument #57 (arahuja)
• Fix bugs with caching and NaN handling #56 (tavinathanson)
• Allow extra keyword arguments in functions #55 (tavinathanson)
• Return 0 for patients with no neoantigens #52 (arahuja)
• Update CHANGELOG.md for 0.1.1 release #51 (arahuja)

0.1.1 (2016-06-14)

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Implemented enhancements:

• Cache a dependency manifest #15
• Refactor how functions work #36 (tavinathanson)
• Pass kwargs through to function #34 (tavinathanson)
• Clarify mannwhitney sidedness #27 (tavinathanson)

Fixed bugs:

• Fix versioneer releasing #20
• Fix RNA BAM path #30 (tavinathanson)

Closed issues:

• additional data assumes patient id field #44
• Is verify_cache still needed? #25
• Fix isovar git dependency #23

Merged pull requests:

• Add mutect and strelka specific variant stats parsing #50 (arahuja)
• Add ability to filter variants #49 (arahuja)
• Refactor plot_benefit #48 (tavinathanson)
• Upgrade varcode for frameshift error and effects df #47 (arahuja)
• Update building dataframe with additional data #45 (arahuja)
• Remove verify cache functions #42 (arahuja)
• Move polyphen data dump to Cohorts object #41 (tavinathanson)
• Save variant metadata after merging variants #39 (arahuja)
• Add loader for PolyPhen2 annotations #38 (armish)
• Update requirements #33 (tavinathanson)
• Add plotting for ROC curve #32 (arahuja)
• Add docstring for load variant functions #31 (arahuja)
• Update isovar setup link #29 (arahuja)
• Add basic provenance tracking #28 (tavinathanson)
• Update README.md #24 (arahuja)
• Fix dataframe loading bug #22 (tavinathanson)
• add CHANGELOG.md #21 (arahuja)

0.1.0 (2016-05-03)

Implemented enhancements:

• Refactor cohorts #14 (tavinathanson)

Fixed bugs:

• Possible issue: sample_id as int vs str #1

Closed issues:

• Warning on import #13

Merged pull requests:

• Update versioning to use versioneer #12 (arahuja)
• Set version in accesible variable #10 (arahuja)
• Add tests, Travis, etc. #9 (tavinathanson)
• Adding comments to plotting functions #8 (arahuja)
• Fix KM plot axis #7 (arahuja)
• Add lifelines as a dependency #6 (armish)
• Add stripboxplot #5 (tavinathanson)
• Handle PFS better #4 (tavinathanson)
• Add easy plotting for cohorts #3 (tavinathanson)
• Add topiary to the requirements #2 (armish)

* This Change Log was automatically generated by github_changelog_generator